› 4k7o

X-ray diffraction
1.98Å resolution

HUMAN PEROXIREDOXIN 5 with a fragment

Released:
DOI: 10.2210/pdb4k7o/pdb
PDB entry 4k7o coloured by chain, front view.
PDB entry 4k7o coloured by chain, side view.
PDB entry 4k7o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Comparing binding modes of analogous fragments using NMR in fragment-based drug design: application to PRDX5.
Aguirre C, ten Brink T, Guichou JF, Cala O, Krimm I
PLoS One 9 e102300 (2014)
PMID: 25025339

Function and Biology Details

Reaction catalysed: 
Thioredoxin + ROOH = thioredoxin disulfide + H(2)O + ROH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-151615 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peroxiredoxin-5, mitochondrial Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 168 amino acids
Theoretical weight: 17.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P30044 (Residues: 54-214; Coverage: 75%)
Gene names: ACR1, PRDX5, SBBI10
Sequence domains: Redoxin
Structure domains: Glutaredoxin

Ligands and Environments

2 bound ligands:
Ligand EKZ 3 x EKZ
Ligand DMS 4 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: C2221
Unit cell:
a: 84.96Å b: 101.55Å c: 148.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.176 0.217
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Concepts and Core Principles of Fragment-Based Drug Design.
Kirsch et al. (2019)
1 more

5 mentions without citation

Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities.
Bolduc et al. (2021)
4 more